TERRAFORMING TERRA
We discuss and comment on the role agriculture will play in the containment of the CO2 problem and address protocols for terraforming the planet Earth.
A model farm template is imagined as the central methodology. A broad range of timely science news and other topics of interest are commented on.

Tuesday, August 30, 2011

First Life Replication

We are now a lot closer to
replicating the first steps in the natural emergence of life.In fact it is now apparent that the precursors
can certainly arise on any new planet.I
also suspect that form and function turns up to be highly conserved.

What is truly astounding is that
life is self emergent everywhere if given the slightest chance.Thus we can safely predict life on every
prospective planet including Mars and eventually Venus (Too internally hot yet
and no water available we have been able to detect.)

It is no surprise to see the
prominence of clay as that is a degraded form of solid crystalline acid.

Life must have begun with a simple molecule that could reproduce
itself – and now we think we know how to make one

4 BILLION years before present: the surface of a newly formed planet
around a medium-sized star is beginning to cool down. It's a violent place,
bombarded by meteorites and riven by volcanic eruptions, with an atmosphere
full of toxic gases. But almost as soon as water begins to form pools and
oceans on its surface, something extraordinary happens. A molecule, or
perhaps a set of molecules, capable of replicating itself arises.

This was the dawn of evolution. Once the first self-replicating
entities appeared, natural selection kicked in, favouring any offspring with
variations that made them better at replicating themselves. Soon the first
simple cells appeared. The rest is prehistory.

Billions of years later, some of the descendants of those first cells
evolved into organisms intelligent enough to wonder what their very earliest
ancestor was like. What molecule started it all?

As far back as the 1960s, a few of those intelligent organisms began to
suspect that the first self-replicating molecules were made of RNA, a close
cousin of DNA. This idea has always had a huge problem, though - there was no
known way by which RNA molecules could have formed on the primordial Earth. And
if RNA molecules couldn't form spontaneously, how could self-replicating RNA
molecules arise? Did some other replicator come first? If so, what was it? The
answer is finally beginning to emerge.

When biologists first started to ponder how life arose, the question
seemed baffling. In all organisms alive today, the hard work is done by
proteins. Proteins can twist and fold into a wild diversity of shapes, so they
can do just about anything, including acting as enzymes, substances that
catalyse a huge range of chemical reactions. However, the information needed to
make proteins is stored in DNA molecules. You can't make
new proteins without DNA, and you can't make new DNA without proteins.
So which came first, proteins or DNA?

The discovery in the 1960s that RNA could fold like a protein, albeit
not into such complex structures, suggested an answer. If RNA could catalyse
reactions as well as storing information, some RNA molecules might be capable
of making more RNA molecules. And if that was the case, RNA replicators would
have had no need for proteins. They could do everything themselves.

After that the floodgates opened. People discovered ever more RNA
enzymes in living organisms and created new ones in their labs. RNA might be
not be as good for storing information as DNA, being less stable, nor as
versatile as proteins, but it was turning out to be a molecular jack of all
trades. This was a huge boost to the idea that the first life consisted of RNA
molecules that catalysed the production of more RNA molecules - "the RNA
world", as Harvard chemist Walter Gilbert dubbed it 25 years ago (Nature, vol 319, p
618).

These RNA replicators may even have had sex. The RNA enzyme Cech
discovered did not just catalyse any old reaction. It was a
short section of RNA that could cut itself out of a longer chain. Reversing
the reaction would add RNA to chains, meaning RNA replicators might have been
able to swap bits with other RNA molecules. This ability would greatly
accelerate evolution, because innovations made by separate lineages of
replicators could be brought together in one lineage.

Still, some issues remained. For one thing, it remained unclear whether
RNA really was capable of replicating itself. Nowadays, DNA and RNA need the help
of many proteins to copy themselves. If there ever was a self-replicator, it
has long since disappeared. So biochemists set out to make one, taking random
RNAs and evolving them for many generations to see what they came up with.

By 2001, this process had yielded an RNA enzyme called R18 that could
stick 14 nucleotides - the building blocks of RNA and DNA - onto an existing
RNA, using another RNA as a template (Science, vol
292, p 1319). Any self-replicating RNA, however, needs to build RNAs that
are at least as long as itself - and R18 doesn't come close. It is 189
nucleotides long, but the longest RNA it can make contains just 20.

A big advance came earlier this year, when Philipp Holliger of the MRC
Laboratory of Molecular Biology in Cambridge,
UK, and
colleagues unveiled an RNA enzyme called tC19Z.
It reliably copies RNA sequences up to 95 letters long, almost half as long as
itself (Science,
vol 332, p 209). To do this, tC19Z clamps onto the end of an RNA, attaches
the correct nucleotide, then moves forward a step and adds another. "It
still blows my mind that you can do something so complex with such a simple
molecule," Holliger says.

So biologists are getting tantalisingly close to creating an RNA
molecule, or perhaps a set of molecules, capable of replicating itself. That
leaves another sticking point: where did the energy to drive this activity come
from? There must have been some kind of metabolic process going on - but RNA
does not look up to the job of running a full-blown metabolism.

"There's been a nagging issue of whether RNA can do all the
chemistry," says Adrian Ferré-D'Amaré of
the National Heart, Lung and Blood Institute in Bethesda, Maryland.
RNA has only a few chemically active "functional groups", which limit
it to catalysing just a few types of chemical reaction.

Functional groups are like tools - the more kinds you have, the more
things you can do. Proteins have many more functional groups than RNAs.
However, there is a way to make a single tool much more versatile: attach
different bits to it, like those screwdrivers that come with interchangeable
heads. The chemical equivalents are small helper molecules known as cofactors.

Proteins use cofactors to extend even further the range of reactions
they can control. Without cofactors, life as we know it couldn't exist,
Ferré-D'Amaré says. And it turns out that RNA enzymes can use cofactors too.

In 2003, Hiroaki Suga, now at the University
of Tokyo, Japan, created an RNA enzyme that
could oxidise alcohol, with help from a cofactor called NAD+ which is used by
many protein enzymes (Nature Structural Biology, vol 10, p 713). Months later,
Ronald Breaker of YaleUniversity found that a
natural RNA enzyme, called glmS, also uses a
cofactor.

Many bacteria use glmS, says Ferré-D'Amaré, so either it is ancient or
RNA enzymes that use cofactors evolve easily. Either way, it looks as if RNA
molecules would have been capable of carrying out the range of the reactions
needed to produce energy.

So the evidence that there was once an RNA world is growing ever more
convincing. Only a
few dissenters remain. "The naysayers about the RNA world have lost a
lot of ground," says Donna Blackmond of the Scripps Research Institute in La Jolla, California.
But there is still one huge and obvious problem: where did the RNA come from in
the first place?

RNA molecules are strings of nucleotides, which in turn are made of
a sugar with a base and a phosphate attached. In living cells, numerous enzymes
are involved in producing nucleotides and joining them together, but of course
the primordial planet had no such enzymes. There was clay, though. In 1996,
biochemist Leslie Orgel showed that when "activated" nucleotides -
those with an extra bit tacked on to the phosphate - were added to a kind of
volcanic clay, RNA molecules up to 55 nucleotides long formed (Nature, vol 381, p
59). With ordinary nucleotides the formation of large RNA molecules would
be energetically unfavourable, but the activated ones provide the energy needed
to drive the reaction.

This suggests that if there were plenty of activated nucleotides on the
early Earth, large RNA molecules would form spontaneously. What's more,experiments
simulating conditions on the early Earth and on asteroids show that sugars,
bases and phosphates would arise
naturally too. It's putting the nucleotides together that is the hard bit;
there does not seem to be any way to join the components without specialised
enzymes. Because of the shapes of the molecules, it is almost impossible for
the sugar to join to a base, and even when it does happen, the combined
molecule quickly breaks apart.

It is here I would
now call upon the ever present solid crystalline acids as a readily available
template and anvil that is capable of energizing the formation of the increasingly
complex molecules.

This apparently insurmountable difficulty led many biologists to
suspect to RNA was not the first replicator after all. Many began exploring the
possibility that the RNA world was preceded by a TNA world, or a PNA world, or
perhaps an ANA world. These are all molecules similar to RNA but whose basic
units are thought to have been much more likely to form spontaneously. The big
problem with this idea is that if life did begin this way, no evidence of it
remains. "You don't see a smoking gun," says Gerald Joyce, also of
the Scripps Research Institute.

In the meantime John Sutherland, at the MRC Laboratory of Molecular
Biology, has been doggedly trying to solve the nucleotide problem. He realised
that researchers might have been going about it the wrong way. "In each
nucleotide, you see a sugar, a base and a phosphate group," he says.
"So you assume you need to make those building blocks first and then stick
them together... and it doesn't work."

Instead he wondered whether simpler molecules might assemble into a
nucleotide without ever becoming sugars or bases. In 2009, he proved it was
possible. He took half a sugar and half a base, and stuck them together -
forming the crucial sugar-base link that everyone had struggled with. Then he
bolted on the rest of the sugar and base. Sutherland stuck on the phosphate
last, though he found that it needed to be present in the mixture for the
earlier reactions to work (Nature, vol 459, p 239).

Goldilocks chemistry

Sutherland was being deliberately messy by including the phosphate from
the start, but it gave the best results. That's encouraging: the primordial
Earth was a messy place and it may have been ideal for making nucleotides.
Sutherland now suspects there
is a "Goldilocks chemistry" - not too simple,
not too complex - that would produce many key compounds from the same melting
pot.

"Sutherland had a real breakthrough," Holliger says.
"Everyone else was barking up the wrong tree."

The issue isn't entirely solved yet. RNA has four different
nucleotides, and so far Sutherland has only produced two of them. However, he
says he is "closing in" on the other two. If he succeeds, it will
show that the spontaneous formation of an RNA replicator is not so improbable
after all, and that the first replicator was most likely made of RNA.

Many questions remain, of course. Where did the first replicators
arise? What was the first life like? How did the transition to DNA and
proteins, and the development of the genetic code, occur? We may never know for
sure but many promising avenues are being explored. Most biologists think there
must have been something like a cell right from the start, to contain the
replicator and keep its component parts together. That way, individuals could
compete for resources and evolve in different ways.

Here
the natural precursor for a call is an oil droplet concept that attaches a
protective cover.That is not so
difficult to simulate0.

Another idea is that life
began in alkaline hydrothermal vents on the sea floor. Not only are these vents
laced with pores and bubbles, but they also provide the same kind of
electrochemical gradient that drives energy production in cells to this day.
Conditions may have been ideal for producing long RNA chains.

Holliger has a rather surprising idea: maybe it all happened in ice. At
the time life began, the sun was 30 per cent dimmer than today. The planet
would have frozen over if the atmosphere hadn't been full of greenhouse gases,
and there may well have been ice towards the poles.

Cold RNA lasts longer, and ice has many other benefits. When water
laced with RNA and other chemicals is cooled, some of it freezes while the rest
becomes a concentrated brine running around the ice crystals. "You get
little pockets within the ice," Holliger says. Interestingly, the R18
RNA enzyme works better in ice than at room temperature (Nature Communications,
DOI: 10.1038/ncomms1076).

Right now, there's no way to choose between these options. No
fossilised vestiges remain of the first replicators as far as we know. But we
can try recreating the RNA world to demonstrate how it might have arisen. One
day soon, Sutherland says, someone will fill a container with a mix of
primordial chemicals, keep it under the right conditions, and watch life
emerge. "That experiment will be done."

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About Me

Apr 2017 - 4.1 Mil Pg Views, March 2013 - Posted my paper introducing CLOUD COSMOLOGY & NEUTRAL NEUTRINO rigorously described as the SPACE TIME PENDULUM, September 2010 I am pleased to report that my essay titled A NEW METRIC WITH APPLICATIONS TO PHYSICS AND SOLVING CERTAIN HIGHER ORDERED DIFFERENTIAL EQUATIONS' has been published in Physics Essays(AIP) and appeared in their June 2010 quarterly. 40 years ago I took an honors degree in applied mathematics from the University of Waterloo. My interest was Relativity and my last year there saw me complete a 900 level course under Hanno Rund on his work in relativity,as well as differential geometry(pure math) and of course analysis. I continued researching new ideas and knowledge since that time and I have prepared a book for publication titled Paradigms Shift&. I maintain my blog as a day book and research tool to retain data and record impressions and interpretations on material read. Do join my blog and receive Four items of interest daily Monday through Saturday.